Hartley was missing from the Saints XV for the Premiership champions' 19-12 victory over London Irish on Sunday.
That led to fears the hooker could be unavailable for England's clashes with New Zealand, South Africa, Samoa and Australia next month.
However, Mallinder has moved to allay fears about the 28-year-old's fitness.
"He's got a sore back - he did it passing the ball from the base of the scrum, so it wasn't a contact injury," Mallinder told BBC Radio Northampton.
"Sometimes it is a bit frustrating, those things, and they take a bit of time. He trained Tuesday and he did it Wednesday morning."
Hartley's availability will be a relief to England coach Stuart Lancaster, who is already without Hartley's fellow hooker Tom Youngs as the Leicester Tigers man has a shoulder injury.
Dan Cole, Mako Vunipola, Alex Corbisiero and Tom Johnson are also unavailable for the November matches due to injury.